Bond and Understanding
by fourze77
Summary: A few month has past since the fall of Messiah. Lacus has became the Chairwoman of the Supreme Council while Kira became ZAFT commander and Athrun became admiral of the Orb forces. What will happen if an alien was recovered near the PLANT. Will they be able to fend off the invasion? An unknown organisation with the most advanced technology appeared out of nowhere came to aid them.
1. Huge Discovery

**I do not own the Gundam Seed or Gundam 00. **

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><p><strong>Bond and Understanding<strong>

**Cosmic Era 73**

Kira Yamato, 18, wearing his white ZAFT uniform showing his high rank in the ZAFT forces. Most of the PLANT Supreme Councils were wondering what his relationship to the Chairwoman Lacus Clyne was. Some of her personal guard such as Yzak Joule, Dearka Elsman and some others already knew their relationship as Kira was not only her personal guard but also her lover. Kira joined ZAFT after the end of the Second Bloody Valentine war. Kira was known to the PLANT as one of the finest mobile suit pilot.

One day, Kira and Lacus went to attend a military meeting with the other ZAFT officers to discussed about the some pieces of the fragments which was found floating near PLANT. Much to his surprise the Representative of the Orb Union, Cagali Yula Atha, who was also his twin sister and the Orb's military officers were also present during the meeting. He noticed that a blue hair officer standing besides Cagali as Athrun Zala, his best friend. They shook hands as soon as Kira arrived along with Lacus. As they took their seat, one of ZAFT officers stood up and began explaining about the fragments.

"As you all know that on February 23 at 6:00 our scouts had discovered as mystery fragments floating around the space which we had retrieved to the PLANT please look at the screen, ladies and gentlemen." said the officer as the images of the fragments appeared on the screen.

"What are those?" asked Athrun.

"We believe it is some kind of transportation as we recovered the pilot." said the officers.

The screen showed the images of the pilot which was a humanoid being about as tall as the human. The figure has almost the same characteristic as the human except it does not possess even as single hair. The life sign shown that it is still breathing but unconscious for the moment. The officers began explaining further the detail.

"It is an alien!" said Cagali in shocked.

"It seems that way, milady. Codename HO." said the officer.

"What is a HO?" asked Cagali.

"HO stands for Humanoid Organism, milady. However we also found foreign languages written on every pieces the fragments."added the officer.

"Do you know what those writing mean?"asked Lacus.

"Unfortunately, milady, we are not able to translate those language even using our most advance translator was not able to translate a single word." said the officer.

"Can you show us the fragments?" asked Athrun.

"Please wait a second,sir." said the officer as he called the scientists to bring the fragments in via com-link.

The scientists came in with a piece of the fragment being placed in a huge glass which was being brought in by the ZAFT staffs. The fragment was placed in the middle so that everyone can see it.

"So this is the fragments." said Athrun.

"Yes,sir." said the officer.

"What do you think Lacus?" asked Kira.

"From the looks of it, it look pretty advance compare to ours." added the officer.

Suddenly, HO awake and its eyes is turquoise in colour. It roared as if it was screaming in pain. It struggled trying to escape the lab where it was kept but the scientists held it as long as they can before they being thrown away by the figure's superhuman strength. As the scientists fell unconscious, one of them managed to activate the alarm before he passed out. HO managed to escape the lab but lost its way at the hallway because the PLANT was big. A guard came to check what happen at lab before being absorbed by the HO. It change its form to match the guard appearance and gained the some of the guard knowledge. It learned about a new mobile suit which was kept at a secret hangar. It ran towards the hangar but was confronted by the guards as they request for its ID. HO was not able to show its ID due to shape shifting ability which can only copy the appearance but not the items. The guards as pointed their rifles at it but they were too late because HO was using it ice breathing ability to freeze the guards. It went into the ZGMF 0056 Chronos and hacked into the system and overwrite it within minutes. It took the Chronos and flew out from the PLANT heading towards to its home planet but HO couldn't flew Chronos very well due its injury. ZAFT forces chased it but HO managed to outrun thanks to Chronos new modified thrusters. It stopped near Jupiter to ask for help from its kind via telepathy.

A guard came into the meeting. As soon as he arrived, he took a breath before told everyone in the meeting about HO had escaped the lab.

"What is the meaning of this? Explain yourself, soldier." said one of the PLANT Supreme Council as he demanded answer.

"S...Sir...H...HO...has escape, sir." said the guard as he gasped for air.

"What? Is it true?" asked Cagali.

"Yes, milady. It even managed to steal the new developed mobile suits at the hangar. When we came in, most of the staffs were froze and they almost lost their lives due to low surrounding temperature. We even send a team to pursue the HO but it also managed to outran us and we lost both visual and signal." explained the guard.

"Can you communicate with it?" asked Lacus.

"Unfortunately, milady, it doesn't understand our language as it thinks that we were the hostile so it shot down one of our man." said the guard.

"We need to find a way to communicate with it. Please find a way." said Lacus.

"Yes, ma'am." said the officer.


	2. New Information

**Anno Domini 2216**

A few weeks had passed since the ELS humanity were able to build a mutual relationship with the ELS. It had been foretold by Aeolia Schenberg that if humanity still having conflicts, it will only spread a spark of conflicts throughout the universe. He founded Celestial Being and gave the technology to the organisation before he put himself in a cold slept which located and guarded by VEDA, his supercomputer which he uploaded his plan for the future. The plan was succeeded but he lost his life during the 'Fallen Angel' incident which he was killed by the traitor. However, his legacy live on throughout the entire Celestial Being as well as the Fereshte. Every members who are still loyal to him carried out his will. After the ELS Conflicts, it was also had been foretold by Aeolia Schenberg that if humanity united and had mutual understanding, they were able to coexist with the other beings. Celestial Being have been declared as the heroes of mankind for uniting the world and achieved mutual understanding with the ELS. The world was at peace. Everyone seem to be happy as humanity will now able to live with the new environment with the ELS.

**Near the moon**

"Miss Sumeragi, we pick up something on our E-sensor." said Millenia Vasti.

"What...Get me a visual." said Sumeragi Lee Noriega.

"Yes, ma'am." added Feldt Grace.

The visual appeared on their main screen. It revealed an object which emiting the GN particles and it's heading toward the Ptolemaios at a great speed. As the object came closer, a Gundam type mobile suit appeared. Everyone were shocked as they recognised the Gundam.

"Isn't that..." said Lasse Aeon.

"Yeah. 00 Quan[T]! He came back." said Millenia's father, Lan Vasti.

"Thank God." said Feldt as she cried because she glad her crush made back to Ptolemy safe.

"00 Quan[T] prepare to dock" said Millenia.

"Roger." said the pilot.

After the 00 Quan[T] docked, Feldt came to the hangar to greet the pilot. The pilot came out from the Gundam. He saw Lan and Feldt waiting in front of the cockpit. They were happy to see him came back still in one piece.

"Welcome back, Setsuna." said Feldt to the pilot with a smile.

"Glad you're back." said Lan.

"Yea, I'm home." said Setsuna F. Seiei as he took off his helmet which shock the two due to his new appearance.

As Setsuna left the hangar, Feldt followed him as they went to meet their expert tactician. Lan looked at 00 Quan[T] as the Gundam had a few different as he thought about the last time he saw it. As Setsuna came into the briefing room, the crews were happy to see him.

"Welcome back, Set-" said Lasse before he stopped due to a shock to see Setsuna's metallic appearance.

"I'll explain." said Tieria Erde as he appeared on the screen.

"What happened to him?" Sumeragi asked Tieria about Setsuna.

"When we achieved mutual understanding during ELS Conflicts, they merged with the 00 Quan[T] and using their bio-technology, they also merged with Setsuna giving him a new regeneration ability which he can regenerate his body in a second and his quantum brainwaves also increase which he can use his quantum brainwaves far greater than any normal Innovators. Setsuna is now a hybrid one due to half of his body is an Innovator while the other half is made of ELS. It's also as a sign of peace between two races." explained Tieria.

Suddenly, 00 Quan[T] GN Drives activated on its own. This caused the hangar to be filled with GN particles. Lan contacted Sumeragi to informed her about the incident. Suddenly, Setsuna felt something and the images flew into his mind as he screamed in pain due the brainwaves was not from ELS but other beings. He screamed in pain for a while before collapsed due to a brain damage. He was taken to the sickbay by the meisters.

"What happened Tieria? I thought you said he was able to regenerate his body immediately." said Sumeragi as everyone was shocked.

"Maybe he consumed too much images than his brain could handle just like the last time. However, I was able to recovered those information. VEDA is now processing the information. We might be able to discovered something." said Tieria.

"I hope Setsuna will be fine." added Sumeragi as she the unconscious Setsuna lying in the sickbay.

"The information has been processed. Please read it, Miss Sumeragi." said Tieria as he sent the data to the Ptolemy.

"This is?" said Sumeragi as she became shocked after read the data.

"Yeah, it seem to me a distress signal but the strange thing is that it's not from this universe." said Tieria.

"Tieria, can we travel to the other universe using Ptolemy?" asked Sumeragi.

"Yes, VEDA has approved the plan. I'm sending the blueprints to Lan. It about a device which allow us to travel anywhere." added Tieria.

**Three days later**

"It's done, dear." said Lan's wife, Linda Vasti.

"Yeah, with this we're able find the mystery distress signal." said Lan in joy.

"Lan, are they ready?" asked Sumeragi.

"Yes." said Lan.

"Everyone, get to your seat and brace for impact." said Sumeragi to the crews.

"Lan, do it." added Sumeragi.

"Roger." said Lan as he activated the device. A bright flash appeared and vanished transported the Ptolemy to the other universe.


	3. New Enemy

**ZAFT Military Base**

As Kira and Lacus were discussing about the incident with Cagali and Athrun as they moving toward with the hangar where the crime scene took place. Lacus' bodyguards followed behind them .They saw a newly built battleship at the hangar. They went to look at it from the bridge above the hangar. Kira was amused at the ship which was built based on Eternal and Archangel.

"That's LHM-GG09 Pluto built based on Eternal and Archangel. That ship is yours, Kira. " said Lacus as she smiled.

"You're giving it to me?" asked Kira.

"Yes, you'll need when you want to go Earth or anywhere." said Lacus.

"You're great, Kira." said Cagali in excitement.

"Well, looks like someone has his own warship. Impressive." said Athrun as he teased Kira.

"Stop it, Athrun." said Kira.

"However, I can't believe ZAFT managed to built that machine so fast." said Cagali.

"That's because we had the best team assigned on the project." said Lacus.

They continued moving till they reached the crime scene.

**Hangar**

As they came in,they saluted with the ZAFT soldiers. They also met with Shinn and most of the ex-Minerva crews who apparently became Pluto's crews. Most of them were happy were happy to the heroes and their idol. Some of them took the opportunity to get an autograph from Lacus.

"What is the situation, everyone?" asked Lacus.

"Lady Lacus, we just found some of these at the crime scene." said one of the ZAFT soldiers as they handing over the evidence to Lacus and the others.

"This is?' wondered Athrun.

"It seems like some kind of chemical liquid but please be careful with it as it is corrosive." said the ZAFT soldier.

"Well, it seems to me like a blood. What do you think, Cagali?" said Kira to his twin.

"It looks sticky to me." said Cagali in disgusted tone.

Later

The alarm has activated which caused them to surprise. A ZAFT soldier reported to them via com-link.

"Lady Lacus, there are unknowns heading toward PLANT. Please get to safety with the Representative of Orb." said Yzak.

"I'll aboard Eternal with Cagali. Arthur, you take control of Pluto as Kira second-in-command." said Lacus.

"Yes, milady!" said Arthur Trine as he saluted to Lacus.

"We should deployed too. Let's go everyone." said Kira.

"Roger!" said the mobile suit pilots.

"It's a good thing a brought Justice along." said Athrun.

"Then, let's go, Athrun." said Kira.

"Right behind you." added Athrun.

As the pilots got into their mobile suits, the hatch opened.

"Lunamaria Hawke, Survive, taking off."

"Shinn Asuka, Destiny, taking off."

"Kira Yamato, Freedom, taking off."

"Athrun Zala, Justice, taking off."

****Near PLANT****

As the mobile suits were assembled outside PLANT. ZAFT forces were ready to confront the unknowns. Most of them were shocked to see the unknowns.

'What are those?" asked Athrun.

"There are many of them." said Kira.

"Can we really pull this off, Commander Kira?" said Arthur.

"Relax, Captain, If Commander Kira is here, we won't be having any trouble against those things plus we got Athrun on our side." said Lunamaria.

"Really! These are the unknowns!"said Shinn.

Their optical images revealed the unknowns. They were some mobile suits resembling the stolen unit, Chronos while some of them had the alien figure with each one of them had black in colour which almost invisible space, pairs of hands and legs with sharp claws and also long tails with blades at the end of the them.

"They are ugly if you ask me." said Lunamaria.

"Isn't that Chronos?" said Cagali in shocked.

"It appeared to be dozens of them." said Lacus.

"To think they were able to mass produced those in short amount of time." said Athrun.

"What kind of factory would-" said Lunamaria before she being interrupted by the beams fired from the Chronos units.

"Well, they aren't patience type I see." said Dearka.

The battle started as both sides returning fires to each other. The battle was chaotic as beams and missiles were almost everywhere in the battle zone. The ZAFT forces received high amount of casualties thanks to aliens which the nemies brought with them. The enemies were having the advantages. Suddenly, a jamming occurred on their com-link.

"Sir, something jamming our communication." said the one of ZAFT soldier.

"What-" said the white uniform ZAFT soldier.

"Sir, the Chronos are heading toward Eternal at a high speed." said the ZAFT soldier.

"What?" said Kira in shocked.

"Kira, I'll stop them. You and the others protect the PLANT." said Athrun as he went after the Chronos units.

"Understood." said Kira as he continue firing at the aliens.

As the Chronos was about to fire at Eternal and its crews were scared, a blast came from the above destroying its beam rifle.

'What's that?" said Cagali as the black mobile suit charged and slashed at the Chronos units one by one which shocked those who witnessed it.

"What's that mobile suit?" said Lunamaria.

"It's fast." said Lacus.

"Amazing! One mobile suit can take out the entire army." added Shinn as he was amazed to watch the unknown black mobile suit slashing the aliens.

"I wondered if Earth Alliance has something to do with it." said Cagali.

"What makes me wondering was how can a single mobile suit is able to take out the entire army." said Lacus.

As the battle end with the enemies retreating, the black mobile suit also vanished after the enemies escaped.


	4. Missing Heroes

**Orb**

Regarded from the incident of the stolen mobile suit in ZAFT Military Base, Cagali held an official meeting with the PLANT Supreme Council at the Orb Administration Office. After they greeted each other, each of them took a seat. Athrun began explaining the incident while Kira's team brought the evidence in a glass box and put it on the centre of the table. The video footages showing the culprit who stole the Chronos.

"This is?"

"It appears to be some kind of chemical liquid which contains toxic substances and it is very corrosive."

"What is that?"

"The culprit appeared to be an alien which we called HO."

"An alien! Are you joking?"

"We also would thought that too but it's the fact."

"What does it want?"

"We don't know yet but please look at this."

The screen showing the moment ZAFT guard was knocked out. HO shape-shifted into the guard and ran toward the hangar.

"What?"

"It can shape-shifted."

"Yes, apparently HO not only capable of copying someone appearance, it can also copy the guard memory which it gained some of our knowledge."

"Are we all here a human?"

"It's al-right."

"Yeah, a blood test shall determine whether you are a human or not."

A blood test was carried out and apparently no sign of abnormal detected. After that, an image of a black mobile suit was displayed.

"As you are all aware, this is the mobile suit that took the aliens which we called Xenomorph."

"It's fast and the pilot must be an expert."

"Yes, it's true but please look behind it."

The screen displayed a cone which emitting the orange reddish light at the back the mobile suit.

"What's that?"

"We do not know yet but the fact is that the light is the one we believe to cause the jamming in our communication during the battle.

"Which organisation does it belong to?"

"Not even Morgenroete has that design."

"We will now called this unit Phantom."

"Phantom really? Is there any better name?"

"We called this unit Phantom because it's black in colour and moves very fast which later vanished into thin air the moment Chronos and Xenomorph retreated."

"Is it a friendly unit or foe?"

"We also don't know but the fact that it saves some of ZAFT pilots from being an easy target to the enemies. It's is enough to declared it as a friendly unit."

**Mars, Ptolemy**

"E-sensor beeped as it detected an approaching heat signal.

"E-sensor detecting something. It's Flag. It's Setsuna. He's back." said Feldt in joy.

"Thank goodness." said Sumeragi in relieved.

After the Flag docked, Setsuna went out of the cockpit after Lan greeted him.

"Good job, Setsuna." said Lan.

"Ah!" said Setsuna as he went toward the bridge.

"Man, still the same as ever. But thanks to him, I got the data on the blue and red gundam type mobile suit." added Lan.

Bridge

"How's the mission, Setsuna?" asked Sumeragi.

"I managed to force the Xenomorph to retreated but apparently ZAFT forces suffered too much casualties." explained Setsuna.

"Xenomorph?" wondered Sumeragi.

"Tieria, please." said Setsuna after he contacted Tieria.

"Roger." said Tieria as he displayed the images of the aliens.

"They are scary." said the frightened Mirallia.

"Based on the information I have gathered during the meeting in Orb, we can only detect the imposter by using a blood test." explained Tieria.

"I also heard that ZAFT new warship, Pluto will be heading toward the abandon Space Colony Athena." said Lockon after his image displayed on the screen.

"I got it. Well done, everyone. Continue on gathering more information about the PLANT and Orb status." said Sumeragi.

"Roger." said Tieria and Lockon before they cut off their communication.

**Near Athena**

As Pluto arrived near the abandon colony, it stopped after that.

"We're here, Commander." said Malik Yardbirds.

"Good job, everyone." said Kira.

"So this is Athena." said Athrun.

"Mobile suit pilots, please guard the ship. Athrun and I will investigate the colony. Let's go, Athrun." added Kira.

"Ah! Let's go" said Athrun.

"Commander, please be careful." said Arthur.

"I will, thank you." said Kira.

After Freedom and Justice were deployed, Kira and Athrun went inside Athena while Shinn and the others waited in Pluto.

**Later**

A huge explosion occurred at Athena blowing way everything around it including Pluto. The colony was blown into fragments.

"Freedom and Justice...signal..." said Meyrin as she started crying and couldn't finished her sentences.

"What is it, Meyrin?" asked Lunamaria.

"Onee-chan, their signal...lost." said the crying Meyrin which shocked the entire crews.

"That's impossible!" screamed Shinn as his tears started to flow down while his fist punched the ship's wall.

"Shinn, calm down." said Lunamaria.

"All pilots, deploy and begin the rescue operation." shouted Arthur.

"Roger!" said the pilots before they deployed.

They went to search around the shattered colony and they finally found both Strike Freedom and Infinite Justice which were badly damaged. They them inside Pluto but much to their surprised the cockpits were gone and there were no sign of the pilots anywhere.

"They're gone." said the cried Meyrin.

"How are we going to tell Lady Lacus and Lady Cagali about this?" asked Arthur.

"Yeah, they must be very sad." said Lunamaria.

"Anyone got any ideas?" asked Arthur.

Their sensor began beeping as something went pass by them. They analysed and recognised it as Phantom. Shinn without wasting any time went into his Destiny and flew to confronted the mysterious black mobile suit.


End file.
